R: Plot a Coloured Dendrogram of Link Communities

plotLinkCommDend {linkcomm} | R Documentation

## Plot a Coloured Dendrogram of Link Communities

### Description

This function is called by `plot.linkcomm` to plot a dendrogram of coloured link communities.

### Usage

    plotLinkCommDend(x, col = TRUE, pal = brewer.pal(9, "Set1"),
            height = x$pdmax, right = FALSE, labels = FALSE, plotcut = TRUE,
            droptrivial = TRUE, leaflab = "none", verbose = TRUE, ...)

### Arguments

`x` | An object of class `linkcomm`.
`col` | Logical, whether to add community-specific colours. Defaults to TRUE.
`pal` | A character vector describing a colour palette to be used for colouring the communites in the dendrogram plot. Defaults to `brewer.pal(9, "Set1")`.
`height` | A numerical value specifying the height at which the dendrogram is cut. Defaults to the maximum partition density height.
`right` | Logical, whether to orient the dendrogram to the right. Defaults to FALSE.
`labels` | Logical, whether to include labels in the dendrogram. Defaults to FALSE.
`plotcut` | Logical, whether to display a horizontal line where the dendrogram is cut. Defaults to TRUE.
`droptrivial` | Logical, whether to not colour communities of size 2. Defaults to TRUE.
`leaflab` | A character string describing the leaf labels on the dendrogram. Can be one of `"none"`, `"perpendicular"`, or `"textlike"`. Defaults to `"none"`.
`verbose` | Logical, whether to display the progress of colouring the dendrogram on screen. Defaults to TRUE.
`...` | Additional arguments to be passed to `plot`.

### Details

Here we describe the parameters for plotting coloured dendrograms using:
`plot(x, type = "dend")`

### Value

A dendrogram plot.

### Author(s)

Alex T. Kalinka alex.t.kalinka@gmail.com

### References

Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27, 2011-2012.

### See Also

`plot.linkcomm`

### Examples

    ## Generate graph and extract link communities.
    g <- swiss[,3:4]
    lc <- getLinkCommunities(g)

    ## Plot a coloured dendrogram.
    plot(lc, type = "dend")

[Package linkcomm version 1.0-14 Index]